SCEL

sciellin, the group of LIM domain containing

Basic information

Region (hg38): 13:77535673-77645263

Links

ENSG00000136155 ∙ NCBI:8796 ∙ OMIM:604112 ∙ HGNC:10573 ∙ Uniprot:O95171 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCEL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCEL gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			41	2		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	2	0

Variants in SCEL

This is a list of pathogenic ClinVar variants found in the SCEL region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
13-77555907-C-T		not specified	Uncertain significance (Feb 28, 2023)
13-77556598-A-T		not specified	Uncertain significance (Dec 14, 2023)
13-77556608-C-T		not specified	Uncertain significance (May 11, 2022)
13-77556623-C-G		not specified	Uncertain significance (Jan 25, 2023)
13-77556625-C-T		not specified	Uncertain significance (Dec 19, 2022)
13-77556675-G-C		not specified	Uncertain significance (Aug 04, 2021)
13-77556703-G-A		not specified	Uncertain significance (Mar 21, 2023)
13-77559817-G-A		Moyamoya angiopathy	Likely pathogenic (-)
13-77559836-G-A		not specified	Uncertain significance (Dec 05, 2022)
13-77559848-A-G		not specified	Uncertain significance (Aug 09, 2021)
13-77563849-T-A		not specified	Uncertain significance (Dec 14, 2021)
13-77563871-C-T		not specified	Uncertain significance (May 31, 2023)
13-77567717-G-A		not specified	Uncertain significance (Dec 18, 2023)
13-77567720-A-G		not specified	Uncertain significance (Feb 13, 2024)
13-77569378-G-A		not specified	Uncertain significance (Feb 13, 2023)
13-77572141-C-T		not specified	Uncertain significance (Dec 19, 2022)
13-77572186-G-A		not specified	Uncertain significance (Feb 15, 2023)
13-77572188-C-T		not specified	Uncertain significance (Jun 06, 2022)
13-77591444-G-A		not specified	Uncertain significance (Dec 27, 2023)
13-77591448-A-G		not specified	Uncertain significance (Aug 17, 2021)
13-77597572-G-A		not specified	Uncertain significance (Sep 27, 2022)
13-77599712-T-C		not specified	Uncertain significance (Jul 09, 2021)
13-77602099-C-G		not specified	Uncertain significance (Jun 26, 2023)
13-77602667-G-A		not specified	Uncertain significance (Jun 02, 2023)
13-77602704-C-T		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCEL	protein_coding	protein_coding	ENST00000349847	32	109590

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.58e-21	0.128	125475	1	272	125748	0.00109

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.286	332	347	0.957	0.0000167	4592
Missense in Polyphen		89	100.79	0.88305		1434
Synonymous	1.46	93	113	0.825	0.00000570	1165
Loss of Function	1.50	38	49.4	0.769	0.00000234	623

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0106	0.0106
Ashkenazi Jewish	0.000214	0.000198
East Asian	0.000195	0.000163
Finnish	0.000417	0.000416
European (Non-Finnish)	0.000374	0.000360
Middle Eastern	0.000195	0.000163
South Asian	0.000942	0.000915
Other	0.00117	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function in the assembly or regulation of proteins in the cornified envelope. The LIM domain may be involved in homotypic or heterotypic associations and may function to localize sciellin to the cornified envelope.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.996
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62.1

Haploinsufficiency Scores

• pHI: 0.0815
• hipred: N
• hipred_score: 0.145
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.485

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	High	Medium	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Scel
• Phenotype: normal phenotype

Gene ontology

• Biological process: epidermis development;response to mechanical stimulus;embryo development ending in birth or egg hatching;keratinocyte differentiation;positive regulation of canonical Wnt signaling pathway
• Cellular component: cornified envelope;cytoplasm;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: protein binding;metal ion binding